Ynoa, 23, compiled a 6.38 ERA in 10 appearances (three starts) with the Mets last season after reaching the majors in August.
"Gabriel Ynoa is young, strong, durable and talented," Orioles executive vice president of baseball operations Dan Duquette said in a statement. "Our scouts feel he can develop into a major league starting pitcher by developing a consistent breaking pitch. We look forward to his contributions to the Orioles this season and beyond."
The Orioles designated catcher Francisco Pena for assignment to open up a roster spot. Pena batted .200 in 40 at-bats for Baltimore last season.